Chile and Argentina share a really long border but this border is strongly defined by the Andes Mountains. This mountain range physically separates these two countries and, because of this natural wall, these two countries have incredibly different cultures. (For example, people typically eat dinner at 10 PM in Argentina but cross that border and people eat dinner at 7 PM). And the reason that these cultures are so different is because this physical barrier is truly a challenge to cross over. The Cruce Andino is an experience that helps make that challenge more accessible.
Traveling by bus throughout the Patagonia region allows you to experience the rugged landscape to the fullest. Crossing the border between Chile and Argentina is pretty common down in Southern Patagonia between Ushuaia in Argentina and Puerto Natales in Chile or between Puerto Natales in Chile and El Calafate in Argentina. (You can read more about these experiences here.) These border crossings are typically organized by a transportation company where the drivers help you through the whole process.
About the Cruce Andino

Further north in the Patagonia area, the best place to cross over between the two Lakes Districts of Chile and Argentina is between Bariloche in Argentina and Puerto Varas in Chile. Cruce Andino, through Turisur, is the company that organizes the crossing which includes 3 ferries and 4 buses. They are the only company that performs the crossing in this way.

From a comfort and efficiency standpoint, the company provides porters to transfer your bags from one form of transportation to the next. In addition, you will have guides throughout the whole day to talk about the history and landscape around you.
The route over the mountain is the same one that Che Guevara took when he traveled through South America. (You can read or watch Motorcycle Diaries to learn more about this.) There is an exposition at one of the stops that includes a replica of his motorcycle and a little information about the route he took.

You have the option between doing the full transit over one day or taking your time and making it a longer experience by staying at hotels at some of the different spots and taking in the overall nature. Cruce Andino can help organize all of this with hotel reservations and luggage transfer. You can learn more about all the tours that Cruce Andino provides here.
The Cruce Andino can also be done more economically by biking the portions of the trip that are done by bus. The distance that you will have to hike/bike is 121 kilometers (75 miles) and you will have to provide your own bicycle. The route over the border is the same one that Che Guevara rode over when he toured through South America. You can learn more about the bike and ride here.
The Cruce Andino described below is done from Bariloche to Puerto Varas. The experience can also be done in the other direction, going from Puerto Varas to Bariloche.
The Bus Alternative to the Cruce Andino
If you want to make the trip between the two parts of the Lakes Districts faster and do not care for the beautiful landscapes you will experience, you can do the whole journey by bus, which takes a little over 5 hours.
The Unique Landscapes You Will See
The First Two Ferries In Argentina
During the whole experience, you will take three ferries to cross over various lakes. The first of these ferries occur in Argentina but each of the lakes provide a unique experience, each of which are beautiful.
The first lake, Lago Nahuel Huapi, feels like a boat ride through Switzerland with beautiful mountains all around you.

The second lake, Lago Frias, is filled with a beautiful emerald green water, colored like that due to the minerals in the water that change the color it emits.

The Border Crossing Between Argentina and Chile
At Lago Frias, you will start the process of crossing the border between Argentina and Chile. Here, next to that replica motorcycle, you will find the border patrol office where you will get stamped out of Argentina. Then, you will take a bus, provided to you by Cruce Andino, to go from customs in Argentina to customs in Chile. (This is the portion that you can do by hiking or biking if you want.) Your guide will show you the exact location of the border change between Chile and Argentina. They will point out the highest peak in the area as well as the unique flora and fauna to this Patagonia region.

Then, you will go through the customs office in Chile to officially enter into the country. The Chile border patrol will give you a PDI paper, which you cannot lose during your time in Chile. You need this paper to be able to leave the country and to check into hotels within Chile! After going through customs, you will have the opportunity to find a place to eat in the small town of Peulla. Unfortunately, Chile is incredibly strict about bringing in any food products into the country and you cannot pack your own snacks for this part of the journey.
The Final Ferry Crossing
After grabbing lunch, you will start the final portion of the journey. The third lake that you will traverse, Lago Todos Los Santos, runs adjacent to two enormous volcanos. This region of Chile has a number of volcanoes, some of which are still active, creating a truly unique landscape. This part is the iconic portion of the voyage. This is also the longest of the ferry rides, allowing you to truly take in the landscapes.

Getting to Puerto Varas
After your final ferry, you will take another bus to get to Puerto Varas, your final stop for this portion of your trip. The route will take you between two volcanoes, Volcan Calbuco and Volcan Osorno, which stands over the town of Puerto Varas and is truly an icon for this region of Chile. To best see the volcano pictured below, sit on the right side of the bus.

While you can use Cruce Andino as a means to get from one country to another, you can also slow down and do the traverse as a weekend trip, stopping and staying at some of the mid-points of the journey. The landscapes are wonderful and waking up with these landscapes around you can be a truly unique experience.